Abby Spurdle
2019-Nov-14 20:59 UTC
[R] Remove highly correlated variables from a data frame or matrix
That's assuming your data was returned by head().
Ana Marija
2019-Nov-14 21:18 UTC
[R] Remove highly correlated variables from a data frame or matrix
what would be the approach to remove variable that has at least 2 correlation coefficients >0.8? this is the whole output of the head()> head(calc.rho)rs56192520 rs3764410 rs145984817 rs1807401 rs1807402 rs35350506 rs56192520 1.000 0.976 0.927 0.927 0.927 0.927 rs3764410 0.976 1.000 0.952 0.952 0.952 0.952 rs145984817 0.927 0.952 1.000 1.000 1.000 1.000 rs1807401 0.927 0.952 1.000 1.000 1.000 1.000 rs1807402 0.927 0.952 1.000 1.000 1.000 1.000 rs35350506 0.927 0.952 1.000 1.000 1.000 1.000 rs2089177 rs12325677 rs62064624 rs62064631 rs2349295 rs2174369 rs56192520 0.927 0.927 0.927 0.927 0.709 0.903 rs3764410 0.952 0.952 0.952 0.952 0.728 0.928 rs145984817 1.000 1.000 1.000 1.000 0.771 0.975 rs1807401 1.000 1.000 1.000 1.000 0.771 0.975 rs1807402 1.000 1.000 1.000 1.000 0.771 0.975 rs35350506 1.000 1.000 1.000 1.000 0.771 0.975 rs7218554 rs62064634 rs4360974 rs4527060 rs6502526 rs6502527 rs56192520 0.903 0.903 0.903 0.903 0.903 0.903 rs3764410 0.928 0.928 0.928 0.928 0.928 0.928 rs145984817 0.975 0.975 0.975 0.975 0.975 0.975 rs1807401 0.975 0.975 0.975 0.975 0.975 0.975 rs1807402 0.975 0.975 0.975 0.975 0.975 0.975 rs35350506 0.975 0.975 0.975 0.975 0.975 0.975 rs9900318 rs8069906 rs9908521 rs9908336 rs9908870 rs9895995 rs56192520 0.903 0.268 0.327 0.327 0.327 0.582 rs3764410 0.928 0.276 0.336 0.336 0.336 0.598 rs145984817 0.975 0.309 0.371 0.371 0.371 0.638 rs1807401 0.975 0.309 0.371 0.371 0.371 0.638 rs1807402 0.975 0.309 0.371 0.371 0.371 0.638 rs35350506 0.975 0.309 0.371 0.371 0.371 0.638 rs7211086 rs9905280 rs8073305 rs8072086 rs4312350 rs4313843 rs56192520 0.880 0.268 0.327 0.880 0.880 0.880 rs3764410 0.905 0.276 0.336 0.905 0.905 0.905 rs145984817 0.951 0.309 0.371 0.951 0.951 0.951 rs1807401 0.951 0.309 0.371 0.951 0.951 0.951 rs1807402 0.951 0.309 0.371 0.951 0.951 0.951 rs35350506 0.951 0.309 0.371 0.951 0.951 0.951 rs8069610 rs883504 rs8072394 rs4280293 rs4465638 rs12602378 rs56192520 0.582 0.903 0.582 0.582 0.811 0.302 rs3764410 0.598 0.928 0.598 0.598 0.836 0.311 rs145984817 0.638 0.975 0.638 0.638 0.879 0.344 rs1807401 0.638 0.975 0.638 0.638 0.879 0.344 rs1807402 0.638 0.975 0.638 0.638 0.879 0.344 rs35350506 0.638 0.975 0.638 0.638 0.879 0.344 rs9899059 rs6502530 rs4380085 rs6502532 rs4792798 rs4792799 rs56192520 0.302 0.309 0.834 0.251 0.063 0.063 rs3764410 0.311 0.318 0.858 0.259 0.080 0.080 rs145984817 0.344 0.352 0.902 0.291 0.086 0.086 rs1807401 0.344 0.352 0.902 0.291 0.086 0.086 rs1807402 0.344 0.352 0.902 0.291 0.086 0.086 rs35350506 0.344 0.352 0.902 0.291 0.086 0.086 rs4316813 rs148563931 rs74751226 rs8068857 rs8069441 rs77397878 rs56192520 0.006 0.006 0.006 0.006 0.006 0.006 rs3764410 0.006 0.006 0.006 0.006 0.006 0.006 rs145984817 0.006 0.006 0.006 0.006 0.006 0.006 rs1807401 0.006 0.006 0.006 0.006 0.006 0.006 rs1807402 0.006 0.006 0.006 0.006 0.006 0.006 rs35350506 0.006 0.006 0.006 0.006 0.006 0.006 rs75339756 rs4608391 rs79569548 rs4275914 rs11870422 rs8075751 rs56192520 0.006 0.006 0.006 0.044 0.007 0.004 rs3764410 0.006 0.006 0.006 0.042 0.005 0.005 rs145984817 0.006 0.006 0.006 0.047 0.002 0.015 rs1807401 0.006 0.006 0.006 0.047 0.002 0.015 rs1807402 0.006 0.006 0.006 0.047 0.002 0.015 rs35350506 0.006 0.006 0.006 0.047 0.002 0.015 rs11658904 rs138437542 rs80344434 rs7222311 rs7221842 rs7223686 rs56192520 0.003 0.004 0.004 0.033 0.009 0.000 rs3764410 0.004 0.004 0.004 0.031 0.007 0.000 rs145984817 0.010 0.004 0.004 0.035 0.011 0.005 rs1807401 0.010 0.004 0.004 0.035 0.011 0.005 rs1807402 0.010 0.004 0.004 0.035 0.011 0.005 rs35350506 0.010 0.004 0.004 0.035 0.011 0.005 rs78013597 rs74965036 rs78063986 rs118106233 rs117345712 rs56192520 0.004 0.004 0.004 0.004 0.005 rs3764410 0.004 0.004 0.004 0.004 0.006 rs145984817 0.004 0.004 0.004 0.004 0.005 rs1807401 0.004 0.004 0.004 0.004 0.005 rs1807402 0.004 0.004 0.004 0.004 0.005 rs35350506 0.004 0.004 0.004 0.004 0.005 rs113004656 rs9898995 rs4985718 rs9893911 rs79110942 rs7208929 rs56192520 0.004 0.033 0.033 0.023 0.004 0.023 rs3764410 0.004 0.031 0.031 0.021 0.004 0.021 rs145984817 0.004 0.035 0.035 0.025 0.004 0.025 rs1807401 0.004 0.035 0.035 0.025 0.004 0.025 rs1807402 0.004 0.035 0.035 0.025 0.004 0.025 rs35350506 0.004 0.035 0.035 0.025 0.004 0.025 rs12601453 rs4078062 rs75129280 rs76664572 rs78961289 rs146364798 rs56192520 0.004 0.001 0.004 0.004 0.004 0.004 rs3764410 0.004 0.002 0.004 0.004 0.004 0.004 rs145984817 0.004 0.001 0.004 0.004 0.004 0.004 rs1807401 0.004 0.001 0.004 0.004 0.004 0.004 rs1807402 0.004 0.001 0.004 0.004 0.004 0.004 rs35350506 0.004 0.001 0.004 0.004 0.004 0.004 rs76715413 rs4078534 rs79457460 rs74369938 rs76423171 rs74668400 rs56192520 0 0.004 0.004 0.002 0.004 0.004 rs3764410 0 0.004 0.004 0.001 0.004 0.004 rs145984817 0 0.004 0.004 0.005 0.004 0.004 rs1807401 0 0.004 0.004 0.005 0.004 0.004 rs1807402 0 0.004 0.004 0.005 0.004 0.004 rs35350506 0 0.004 0.004 0.005 0.004 0.004 rs75146120 rs1135237 rs9914671 rs117759512 rs4985696 rs16961340 rs56192520 0.004 0.003 0.009 0.004 0.009 0.004 rs3764410 0.004 0.003 0.007 0.004 0.007 0.004 rs145984817 0.004 0.003 0.011 0.004 0.011 0.004 rs1807401 0.004 0.003 0.011 0.004 0.011 0.004 rs1807402 0.004 0.003 0.011 0.004 0.011 0.004 rs35350506 0.004 0.003 0.011 0.004 0.011 0.004 rs17794159 rs4247118 rs78572469 rs12601193 rs2349646 rs2090018 rs56192520 0.001 0.033 0.002 0.004 0.020 0.033 rs3764410 0.002 0.031 0.001 0.004 0.019 0.031 rs145984817 0.001 0.035 0.005 0.004 0.022 0.035 rs1807401 0.001 0.035 0.005 0.004 0.022 0.035 rs1807402 0.001 0.035 0.005 0.004 0.022 0.035 rs35350506 0.001 0.035 0.005 0.004 0.022 0.035 rs12601424 rs4985701 rs8064550 rs2271521 rs2271520 rs11078374 rs56192520 0.004 0.033 0.033 0.004 0.033 0.014 rs3764410 0.004 0.031 0.031 0.004 0.031 0.012 rs145984817 0.004 0.035 0.035 0.004 0.035 0.016 rs1807401 0.004 0.035 0.035 0.004 0.035 0.016 rs1807402 0.004 0.035 0.035 0.004 0.035 0.016 rs35350506 0.004 0.035 0.035 0.004 0.035 0.016 rs4985702 rs1124961 rs11652674 rs3924340 rs112450164 rs7208973 rs56192520 0.033 0.003 0.002 0.001 0.004 0.033 rs3764410 0.031 0.003 0.001 0.002 0.004 0.031 rs145984817 0.035 0.003 0.005 0.001 0.004 0.035 rs1807401 0.035 0.003 0.005 0.001 0.004 0.035 rs1807402 0.035 0.003 0.005 0.001 0.004 0.035 rs35350506 0.035 0.003 0.005 0.001 0.004 0.035 rs9910857 rs78574480 rs8072184 rs12602196 rs6502563 rs3744135 rs56192520 0.006 0.004 0.014 0.004 0.033 0.004 rs3764410 0.005 0.004 0.012 0.004 0.031 0.004 rs145984817 0.002 0.004 0.016 0.004 0.035 0.004 rs1807401 0.002 0.004 0.016 0.004 0.035 0.004 rs1807402 0.002 0.004 0.016 0.004 0.035 0.004 rs35350506 0.002 0.004 0.016 0.004 0.035 0.004 rs148779543 rs77689691 rs41319048 rs117340532 rs78647096 rs77712968 rs56192520 0 0.004 0.004 0.002 0.004 0.004 rs3764410 0 0.004 0.004 0.001 0.004 0.004 rs145984817 0 0.004 0.004 0.005 0.004 0.004 rs1807401 0 0.004 0.004 0.005 0.004 0.004 rs1807402 0 0.004 0.004 0.005 0.004 0.004 rs35350506 0 0.004 0.004 0.005 0.004 0.004 rs16961396 rs80054920 rs7206981 rs4985740 rs3803762 rs77103270 rs56192520 0.004 0.004 0.033 0.023 0.004 0.002 rs3764410 0.004 0.004 0.031 0.021 0.004 0.001 rs145984817 0.004 0.004 0.035 0.025 0.004 0.005 rs1807401 0.004 0.004 0.035 0.025 0.004 0.005 rs1807402 0.004 0.004 0.035 0.025 0.004 0.005 rs35350506 0.004 0.004 0.035 0.025 0.004 0.005 rs7207485 rs77342773 rs3826304 rs3744126 rs7210879 rs7211576 rs56192520 0.029 0.004 0.004 0.004 0.023 0.006 rs3764410 0.027 0.004 0.004 0.004 0.021 0.005 rs145984817 0.031 0.004 0.004 0.004 0.025 0.002 rs1807401 0.031 0.004 0.004 0.004 0.025 0.002 rs1807402 0.031 0.004 0.004 0.004 0.025 0.002 rs35350506 0.031 0.004 0.004 0.004 0.025 0.002 rs117967362 rs75978745 rs6502564 rs9894565 rs36079048 rs8076621 rs56192520 0.004 0.004 0.007 0.017 0 0.004 rs3764410 0.004 0.004 0.005 0.015 0 0.004 rs145984817 0.004 0.004 0.009 0.019 0 0.004 rs1807401 0.004 0.004 0.009 0.019 0 0.004 rs1807402 0.004 0.004 0.009 0.019 0 0.004 rs35350506 0.004 0.004 0.009 0.019 0 0.004 rs7218795 rs3803761 rs12602675 rs7208065 rs4985705 rs8080386 rs56192520 0.026 0.032 0 0.018 0.014 0.003 rs3764410 0.024 0.029 0 0.015 0.011 0.002 rs145984817 0.028 0.034 0 0.021 0.016 0.004 rs1807401 0.028 0.034 0 0.021 0.016 0.004 rs1807402 0.028 0.034 0 0.021 0.016 0.004 rs35350506 0.028 0.034 0 0.021 0.016 0.004 rs8065832 rs2018781 rs1736221 rs1736220 rs1736217 rs1708620 rs56192520 0.008 0.039 0.003 0.003 0.021 0.009 rs3764410 0.006 0.037 0.002 0.002 0.019 0.007 rs145984817 0.010 0.042 0.004 0.004 0.024 0.011 rs1807401 0.010 0.042 0.004 0.004 0.024 0.011 rs1807402 0.010 0.042 0.004 0.004 0.024 0.011 rs35350506 0.010 0.042 0.004 0.004 0.024 0.011 rs1708619 rs1736216 rs76319098 rs1736215 rs1736214 rs1708617 rs56192520 0.009 0.024 0.017 0.012 0.019 0.029 rs3764410 0.007 0.021 0.016 0.009 0.016 0.026 rs145984817 0.011 0.026 0.018 0.014 0.022 0.031 rs1807401 0.011 0.026 0.018 0.014 0.022 0.031 rs1807402 0.011 0.026 0.018 0.014 0.022 0.031 rs35350506 0.011 0.026 0.018 0.014 0.022 0.031 rs12602831 rs12602871 rs1736213 rs1736212 rs76045368 rs34518797 rs56192520 0.000 0.000 0.015 0.029 0.001 0.001 rs3764410 0.001 0.001 0.013 0.026 0.001 0.001 rs145984817 0.000 0.000 0.018 0.031 0.000 0.000 rs1807401 0.000 0.000 0.018 0.031 0.000 0.000 rs1807402 0.000 0.000 0.018 0.031 0.000 0.000 rs35350506 0.000 0.000 0.018 0.031 0.000 0.000 rs11078378 rs8079562 rs8065774 rs8066090 rs41337846 rs1736209 rs56192520 0.043 0.001 0.001 0.029 0.000 0.029 rs3764410 0.041 0.001 0.001 0.026 0.001 0.026 rs145984817 0.046 0.000 0.000 0.031 0.000 0.031 rs1807401 0.046 0.000 0.000 0.031 0.000 0.031 rs1807402 0.046 0.000 0.000 0.031 0.000 0.031 rs35350506 0.046 0.000 0.000 0.031 0.000 0.031 rs1736208 rs12949822 rs76246042 rs12600635 rs55689224 rs1736207 rs56192520 0.043 0.043 0.000 0.000 0.000 0.015 rs3764410 0.041 0.041 0.001 0.001 0.001 0.013 rs145984817 0.046 0.046 0.000 0.000 0.000 0.018 rs1807401 0.046 0.046 0.000 0.000 0.000 0.018 rs1807402 0.046 0.046 0.000 0.000 0.000 0.018 rs35350506 0.046 0.046 0.000 0.000 0.000 0.018 rs1708626 rs1736206 rs9896078 rs16961474 rs1708627 rs1736205 rs56192520 0.015 0.015 0.001 0.001 0.017 0.021 rs3764410 0.013 0.013 0.001 0.001 0.014 0.019 rs145984817 0.018 0.018 0.000 0.001 0.020 0.024 rs1807401 0.018 0.018 0.000 0.001 0.020 0.024 rs1807402 0.018 0.018 0.000 0.001 0.020 0.024 rs35350506 0.018 0.018 0.000 0.001 0.020 0.024 rs1708628 rs7220577 rs2294155 rs1736204 rs1736203 rs1736202 rs56192520 0.011 0.011 0.000 0.021 0.014 0.014 rs3764410 0.009 0.009 0.000 0.019 0.011 0.011 rs145984817 0.013 0.013 0.001 0.024 0.016 0.016 rs1807401 0.013 0.013 0.001 0.024 0.016 0.016 rs1807402 0.013 0.013 0.001 0.024 0.016 0.016 rs35350506 0.013 0.013 0.001 0.024 0.016 0.016 rs12937908 rs1736200 rs1708623 rs1708624 rs9894884 rs9901894 rs56192520 0.009 0.009 0.008 0.007 0.009 0.009 rs3764410 0.007 0.007 0.006 0.005 0.007 0.007 rs145984817 0.011 0.011 0.010 0.008 0.011 0.011 rs1807401 0.011 0.011 0.010 0.008 0.011 0.011 rs1807402 0.011 0.011 0.010 0.008 0.011 0.011 rs35350506 0.011 0.011 0.010 0.008 0.011 0.011 rs9903294 rs2472689 rs1630656 rs111478970 rs3182911 rs7219012 rs56192520 0.008 0.011 0.007 0.007 0.008 0.000 rs3764410 0.006 0.009 0.005 0.005 0.006 0.000 rs145984817 0.010 0.013 0.008 0.008 0.010 0.001 rs1807401 0.010 0.013 0.008 0.008 0.010 0.001 rs1807402 0.010 0.013 0.008 0.008 0.010 0.001 rs35350506 0.010 0.013 0.008 0.008 0.010 0.001 rs9890657 rs12453455 rs12947291 rs150267386 rs16961493 rs11652745 rs56192520 0.009 0.007 0.008 0.013 0.000 0.009 rs3764410 0.007 0.005 0.006 0.012 0.000 0.007 rs145984817 0.011 0.008 0.010 0.014 0.001 0.011 rs1807401 0.011 0.008 0.010 0.014 0.001 0.011 rs1807402 0.011 0.008 0.010 0.014 0.001 0.011 rs35350506 0.011 0.008 0.010 0.014 0.001 0.011 rs9907107 rs8070574 rs4985759 rs3866959 rs7219248 rs6502568 rs56192520 0.009 0.009 0.009 0.011 0.009 0.011 rs3764410 0.007 0.007 0.007 0.009 0.007 0.009 rs145984817 0.011 0.011 0.011 0.013 0.011 0.013 rs1807401 0.011 0.011 0.011 0.013 0.011 0.013 rs1807402 0.011 0.011 0.011 0.013 0.011 0.013 rs35350506 0.011 0.011 0.011 0.013 0.011 0.013 rs7220275 rs12450037 rs7225876 rs9892352 rs4985760 rs6502569 rs56192520 0.009 0.008 0.007 0.011 0.011 0.011 rs3764410 0.007 0.006 0.005 0.009 0.009 0.009 rs145984817 0.011 0.010 0.008 0.013 0.013 0.013 rs1807401 0.011 0.010 0.008 0.013 0.013 0.013 rs1807402 0.011 0.010 0.008 0.013 0.013 0.013 rs35350506 0.011 0.010 0.008 0.013 0.013 0.013 rs1029830 rs2012954 rs1029832 rs2270180 rs8072402 rs7221553 rs56192520 0.009 0.011 0.008 0.000 0.009 0.011 rs3764410 0.007 0.009 0.006 0.000 0.007 0.009 rs145984817 0.011 0.013 0.010 0.001 0.011 0.013 rs1807401 0.011 0.013 0.010 0.001 0.011 0.013 rs1807402 0.011 0.013 0.010 0.001 0.011 0.013 rs35350506 0.011 0.013 0.010 0.001 0.011 0.013 rs145597919 rs150772017 rs2041393 rs6502578 rs11078382 rs9912109 rs56192520 0.013 0.013 0.005 0.005 0 0.005 rs3764410 0.012 0.012 0.004 0.004 0 0.004 rs145984817 0.014 0.014 0.006 0.006 0 0.006 rs1807401 0.014 0.014 0.006 0.006 0 0.006 rs1807402 0.014 0.014 0.006 0.006 0 0.006 rs35350506 0.014 0.014 0.006 0.006 0 0.006 rs12601631 rs11869054 rs11869079 rs9912599 rs7220057 rs9896970 rs56192520 0 0 0 0 0 0 rs3764410 0 0 0 0 0 0 rs145984817 0 0 0 0 0 0 rs1807401 0 0 0 0 0 0 rs1807402 0 0 0 0 0 0 rs35350506 0 0 0 0 0 0 rs34121330 rs34668117 rs67773570 rs242252 rs955893 rs28583584 rs56192520 0.000 0.000 0 0.002 0.001 0.013 rs3764410 0.001 0.001 0 0.003 0.001 0.005 rs145984817 0.000 0.000 0 0.002 0.001 0.004 rs1807401 0.000 0.000 0 0.002 0.001 0.004 rs1807402 0.000 0.000 0 0.002 0.001 0.004 rs35350506 0.000 0.000 0 0.002 0.001 0.004 rs9944423 rs7217764 rs11651957 rs73978990 rs8071007 rs56044345 rs56192520 0.013 0.011 0.011 0.011 0.011 0.011 rs3764410 0.005 0.004 0.004 0.004 0.004 0.004 rs145984817 0.004 0.003 0.003 0.003 0.003 0.003 rs1807401 0.004 0.003 0.003 0.003 0.003 0.003 rs1807402 0.004 0.003 0.003 0.003 0.003 0.003 rs35350506 0.004 0.003 0.003 0.003 0.003 0.003 rs17804843 rs56192520 0 rs3764410 0 rs145984817 0 rs1807401 0 rs1807402 0 rs35350506 0 On Thu, Nov 14, 2019 at 2:59 PM Abby Spurdle <spurdle.a at gmail.com> wrote:> > That's assuming your data was returned by head().
Jim Lemon
2019-Nov-14 21:39 UTC
[R] Remove highly correlated variables from a data frame or matrix
I thought you were going to trick us. What I think you are asking now
is how to get the variable names in the columns that have at most one
_absolute_ value greater than 0.8. OK:
# I'm not going to try to recreate your correlation matrix
calc.jim<-matrix(runif(100,min=-1,max=1),nrow=10)
for(i in 1:10) calc.jim[i,i]<-1
rownames(calc.jim)<-<-colnames(calc.jim)<-paste0("rs",1:10)
Now that we have a plausible fake correlation matrix, all we have to
do is extract the column names:
colnames(calc.jim)[colSums(abs(calc.jim)>0.8)<2]
Of course, what you really meant could have been, "I want the column
names of the variables with at most one absolute value greater than
0.8 ignoring the diagonal values because I don't care about those". If
so:
colnames(calc.jim)[colSums(abs(calc.jim)>0.8)<3]
Any more tricks?
Jim
On Fri, Nov 15, 2019 at 8:17 AM Ana Marija <sokovic.anamarija at
gmail.com> wrote:>
> what would be the approach to remove variable that has at least 2
> correlation coefficients >0.8?
> this is the whole output of the head()
>
> > head(calc.rho)
> rs56192520 rs3764410 rs145984817 rs1807401 rs1807402 rs35350506
> rs56192520 1.000 0.976 0.927 0.927 0.927 0.927
> rs3764410 0.976 1.000 0.952 0.952 0.952 0.952
> rs145984817 0.927 0.952 1.000 1.000 1.000 1.000
> rs1807401 0.927 0.952 1.000 1.000 1.000 1.000
> rs1807402 0.927 0.952 1.000 1.000 1.000 1.000
> rs35350506 0.927 0.952 1.000 1.000 1.000 1.000
> rs2089177 rs12325677 rs62064624 rs62064631 rs2349295 rs2174369
> rs56192520 0.927 0.927 0.927 0.927 0.709 0.903
> rs3764410 0.952 0.952 0.952 0.952 0.728 0.928
> rs145984817 1.000 1.000 1.000 1.000 0.771 0.975
> rs1807401 1.000 1.000 1.000 1.000 0.771 0.975
> rs1807402 1.000 1.000 1.000 1.000 0.771 0.975
> rs35350506 1.000 1.000 1.000 1.000 0.771 0.975
> rs7218554 rs62064634 rs4360974 rs4527060 rs6502526 rs6502527
> rs56192520 0.903 0.903 0.903 0.903 0.903 0.903
> rs3764410 0.928 0.928 0.928 0.928 0.928 0.928
> rs145984817 0.975 0.975 0.975 0.975 0.975 0.975
> rs1807401 0.975 0.975 0.975 0.975 0.975 0.975
> rs1807402 0.975 0.975 0.975 0.975 0.975 0.975
> rs35350506 0.975 0.975 0.975 0.975 0.975 0.975
> rs9900318 rs8069906 rs9908521 rs9908336 rs9908870 rs9895995
> rs56192520 0.903 0.268 0.327 0.327 0.327 0.582
> rs3764410 0.928 0.276 0.336 0.336 0.336 0.598
> rs145984817 0.975 0.309 0.371 0.371 0.371 0.638
> rs1807401 0.975 0.309 0.371 0.371 0.371 0.638
> rs1807402 0.975 0.309 0.371 0.371 0.371 0.638
> rs35350506 0.975 0.309 0.371 0.371 0.371 0.638
> rs7211086 rs9905280 rs8073305 rs8072086 rs4312350 rs4313843
> rs56192520 0.880 0.268 0.327 0.880 0.880 0.880
> rs3764410 0.905 0.276 0.336 0.905 0.905 0.905
> rs145984817 0.951 0.309 0.371 0.951 0.951 0.951
> rs1807401 0.951 0.309 0.371 0.951 0.951 0.951
> rs1807402 0.951 0.309 0.371 0.951 0.951 0.951
> rs35350506 0.951 0.309 0.371 0.951 0.951 0.951
> rs8069610 rs883504 rs8072394 rs4280293 rs4465638 rs12602378
> rs56192520 0.582 0.903 0.582 0.582 0.811 0.302
> rs3764410 0.598 0.928 0.598 0.598 0.836 0.311
> rs145984817 0.638 0.975 0.638 0.638 0.879 0.344
> rs1807401 0.638 0.975 0.638 0.638 0.879 0.344
> rs1807402 0.638 0.975 0.638 0.638 0.879 0.344
> rs35350506 0.638 0.975 0.638 0.638 0.879 0.344
> rs9899059 rs6502530 rs4380085 rs6502532 rs4792798 rs4792799
> rs56192520 0.302 0.309 0.834 0.251 0.063 0.063
> rs3764410 0.311 0.318 0.858 0.259 0.080 0.080
> rs145984817 0.344 0.352 0.902 0.291 0.086 0.086
> rs1807401 0.344 0.352 0.902 0.291 0.086 0.086
> rs1807402 0.344 0.352 0.902 0.291 0.086 0.086
> rs35350506 0.344 0.352 0.902 0.291 0.086 0.086
> rs4316813 rs148563931 rs74751226 rs8068857 rs8069441 rs77397878
> rs56192520 0.006 0.006 0.006 0.006 0.006 0.006
> rs3764410 0.006 0.006 0.006 0.006 0.006 0.006
> rs145984817 0.006 0.006 0.006 0.006 0.006 0.006
> rs1807401 0.006 0.006 0.006 0.006 0.006 0.006
> rs1807402 0.006 0.006 0.006 0.006 0.006 0.006
> rs35350506 0.006 0.006 0.006 0.006 0.006 0.006
> rs75339756 rs4608391 rs79569548 rs4275914 rs11870422 rs8075751
> rs56192520 0.006 0.006 0.006 0.044 0.007 0.004
> rs3764410 0.006 0.006 0.006 0.042 0.005 0.005
> rs145984817 0.006 0.006 0.006 0.047 0.002 0.015
> rs1807401 0.006 0.006 0.006 0.047 0.002 0.015
> rs1807402 0.006 0.006 0.006 0.047 0.002 0.015
> rs35350506 0.006 0.006 0.006 0.047 0.002 0.015
> rs11658904 rs138437542 rs80344434 rs7222311 rs7221842 rs7223686
> rs56192520 0.003 0.004 0.004 0.033 0.009 0.000
> rs3764410 0.004 0.004 0.004 0.031 0.007 0.000
> rs145984817 0.010 0.004 0.004 0.035 0.011 0.005
> rs1807401 0.010 0.004 0.004 0.035 0.011 0.005
> rs1807402 0.010 0.004 0.004 0.035 0.011 0.005
> rs35350506 0.010 0.004 0.004 0.035 0.011 0.005
> rs78013597 rs74965036 rs78063986 rs118106233 rs117345712
> rs56192520 0.004 0.004 0.004 0.004 0.005
> rs3764410 0.004 0.004 0.004 0.004 0.006
> rs145984817 0.004 0.004 0.004 0.004 0.005
> rs1807401 0.004 0.004 0.004 0.004 0.005
> rs1807402 0.004 0.004 0.004 0.004 0.005
> rs35350506 0.004 0.004 0.004 0.004 0.005
> rs113004656 rs9898995 rs4985718 rs9893911 rs79110942 rs7208929
> rs56192520 0.004 0.033 0.033 0.023 0.004 0.023
> rs3764410 0.004 0.031 0.031 0.021 0.004 0.021
> rs145984817 0.004 0.035 0.035 0.025 0.004 0.025
> rs1807401 0.004 0.035 0.035 0.025 0.004 0.025
> rs1807402 0.004 0.035 0.035 0.025 0.004 0.025
> rs35350506 0.004 0.035 0.035 0.025 0.004 0.025
> rs12601453 rs4078062 rs75129280 rs76664572 rs78961289
rs146364798
> rs56192520 0.004 0.001 0.004 0.004 0.004
0.004
> rs3764410 0.004 0.002 0.004 0.004 0.004
0.004
> rs145984817 0.004 0.001 0.004 0.004 0.004
0.004
> rs1807401 0.004 0.001 0.004 0.004 0.004
0.004
> rs1807402 0.004 0.001 0.004 0.004 0.004
0.004
> rs35350506 0.004 0.001 0.004 0.004 0.004
0.004
> rs76715413 rs4078534 rs79457460 rs74369938 rs76423171
rs74668400
> rs56192520 0 0.004 0.004 0.002 0.004
0.004
> rs3764410 0 0.004 0.004 0.001 0.004
0.004
> rs145984817 0 0.004 0.004 0.005 0.004
0.004
> rs1807401 0 0.004 0.004 0.005 0.004
0.004
> rs1807402 0 0.004 0.004 0.005 0.004
0.004
> rs35350506 0 0.004 0.004 0.005 0.004
0.004
> rs75146120 rs1135237 rs9914671 rs117759512 rs4985696 rs16961340
> rs56192520 0.004 0.003 0.009 0.004 0.009 0.004
> rs3764410 0.004 0.003 0.007 0.004 0.007 0.004
> rs145984817 0.004 0.003 0.011 0.004 0.011 0.004
> rs1807401 0.004 0.003 0.011 0.004 0.011 0.004
> rs1807402 0.004 0.003 0.011 0.004 0.011 0.004
> rs35350506 0.004 0.003 0.011 0.004 0.011 0.004
> rs17794159 rs4247118 rs78572469 rs12601193 rs2349646 rs2090018
> rs56192520 0.001 0.033 0.002 0.004 0.020 0.033
> rs3764410 0.002 0.031 0.001 0.004 0.019 0.031
> rs145984817 0.001 0.035 0.005 0.004 0.022 0.035
> rs1807401 0.001 0.035 0.005 0.004 0.022 0.035
> rs1807402 0.001 0.035 0.005 0.004 0.022 0.035
> rs35350506 0.001 0.035 0.005 0.004 0.022 0.035
> rs12601424 rs4985701 rs8064550 rs2271521 rs2271520 rs11078374
> rs56192520 0.004 0.033 0.033 0.004 0.033 0.014
> rs3764410 0.004 0.031 0.031 0.004 0.031 0.012
> rs145984817 0.004 0.035 0.035 0.004 0.035 0.016
> rs1807401 0.004 0.035 0.035 0.004 0.035 0.016
> rs1807402 0.004 0.035 0.035 0.004 0.035 0.016
> rs35350506 0.004 0.035 0.035 0.004 0.035 0.016
> rs4985702 rs1124961 rs11652674 rs3924340 rs112450164 rs7208973
> rs56192520 0.033 0.003 0.002 0.001 0.004 0.033
> rs3764410 0.031 0.003 0.001 0.002 0.004 0.031
> rs145984817 0.035 0.003 0.005 0.001 0.004 0.035
> rs1807401 0.035 0.003 0.005 0.001 0.004 0.035
> rs1807402 0.035 0.003 0.005 0.001 0.004 0.035
> rs35350506 0.035 0.003 0.005 0.001 0.004 0.035
> rs9910857 rs78574480 rs8072184 rs12602196 rs6502563 rs3744135
> rs56192520 0.006 0.004 0.014 0.004 0.033 0.004
> rs3764410 0.005 0.004 0.012 0.004 0.031 0.004
> rs145984817 0.002 0.004 0.016 0.004 0.035 0.004
> rs1807401 0.002 0.004 0.016 0.004 0.035 0.004
> rs1807402 0.002 0.004 0.016 0.004 0.035 0.004
> rs35350506 0.002 0.004 0.016 0.004 0.035 0.004
> rs148779543 rs77689691 rs41319048 rs117340532 rs78647096
rs77712968
> rs56192520 0 0.004 0.004 0.002 0.004
0.004
> rs3764410 0 0.004 0.004 0.001 0.004
0.004
> rs145984817 0 0.004 0.004 0.005 0.004
0.004
> rs1807401 0 0.004 0.004 0.005 0.004
0.004
> rs1807402 0 0.004 0.004 0.005 0.004
0.004
> rs35350506 0 0.004 0.004 0.005 0.004
0.004
> rs16961396 rs80054920 rs7206981 rs4985740 rs3803762 rs77103270
> rs56192520 0.004 0.004 0.033 0.023 0.004 0.002
> rs3764410 0.004 0.004 0.031 0.021 0.004 0.001
> rs145984817 0.004 0.004 0.035 0.025 0.004 0.005
> rs1807401 0.004 0.004 0.035 0.025 0.004 0.005
> rs1807402 0.004 0.004 0.035 0.025 0.004 0.005
> rs35350506 0.004 0.004 0.035 0.025 0.004 0.005
> rs7207485 rs77342773 rs3826304 rs3744126 rs7210879 rs7211576
> rs56192520 0.029 0.004 0.004 0.004 0.023 0.006
> rs3764410 0.027 0.004 0.004 0.004 0.021 0.005
> rs145984817 0.031 0.004 0.004 0.004 0.025 0.002
> rs1807401 0.031 0.004 0.004 0.004 0.025 0.002
> rs1807402 0.031 0.004 0.004 0.004 0.025 0.002
> rs35350506 0.031 0.004 0.004 0.004 0.025 0.002
> rs117967362 rs75978745 rs6502564 rs9894565 rs36079048 rs8076621
> rs56192520 0.004 0.004 0.007 0.017 0 0.004
> rs3764410 0.004 0.004 0.005 0.015 0 0.004
> rs145984817 0.004 0.004 0.009 0.019 0 0.004
> rs1807401 0.004 0.004 0.009 0.019 0 0.004
> rs1807402 0.004 0.004 0.009 0.019 0 0.004
> rs35350506 0.004 0.004 0.009 0.019 0 0.004
> rs7218795 rs3803761 rs12602675 rs7208065 rs4985705 rs8080386
> rs56192520 0.026 0.032 0 0.018 0.014 0.003
> rs3764410 0.024 0.029 0 0.015 0.011 0.002
> rs145984817 0.028 0.034 0 0.021 0.016 0.004
> rs1807401 0.028 0.034 0 0.021 0.016 0.004
> rs1807402 0.028 0.034 0 0.021 0.016 0.004
> rs35350506 0.028 0.034 0 0.021 0.016 0.004
> rs8065832 rs2018781 rs1736221 rs1736220 rs1736217 rs1708620
> rs56192520 0.008 0.039 0.003 0.003 0.021 0.009
> rs3764410 0.006 0.037 0.002 0.002 0.019 0.007
> rs145984817 0.010 0.042 0.004 0.004 0.024 0.011
> rs1807401 0.010 0.042 0.004 0.004 0.024 0.011
> rs1807402 0.010 0.042 0.004 0.004 0.024 0.011
> rs35350506 0.010 0.042 0.004 0.004 0.024 0.011
> rs1708619 rs1736216 rs76319098 rs1736215 rs1736214 rs1708617
> rs56192520 0.009 0.024 0.017 0.012 0.019 0.029
> rs3764410 0.007 0.021 0.016 0.009 0.016 0.026
> rs145984817 0.011 0.026 0.018 0.014 0.022 0.031
> rs1807401 0.011 0.026 0.018 0.014 0.022 0.031
> rs1807402 0.011 0.026 0.018 0.014 0.022 0.031
> rs35350506 0.011 0.026 0.018 0.014 0.022 0.031
> rs12602831 rs12602871 rs1736213 rs1736212 rs76045368 rs34518797
> rs56192520 0.000 0.000 0.015 0.029 0.001 0.001
> rs3764410 0.001 0.001 0.013 0.026 0.001 0.001
> rs145984817 0.000 0.000 0.018 0.031 0.000 0.000
> rs1807401 0.000 0.000 0.018 0.031 0.000 0.000
> rs1807402 0.000 0.000 0.018 0.031 0.000 0.000
> rs35350506 0.000 0.000 0.018 0.031 0.000 0.000
> rs11078378 rs8079562 rs8065774 rs8066090 rs41337846 rs1736209
> rs56192520 0.043 0.001 0.001 0.029 0.000 0.029
> rs3764410 0.041 0.001 0.001 0.026 0.001 0.026
> rs145984817 0.046 0.000 0.000 0.031 0.000 0.031
> rs1807401 0.046 0.000 0.000 0.031 0.000 0.031
> rs1807402 0.046 0.000 0.000 0.031 0.000 0.031
> rs35350506 0.046 0.000 0.000 0.031 0.000 0.031
> rs1736208 rs12949822 rs76246042 rs12600635 rs55689224 rs1736207
> rs56192520 0.043 0.043 0.000 0.000 0.000 0.015
> rs3764410 0.041 0.041 0.001 0.001 0.001 0.013
> rs145984817 0.046 0.046 0.000 0.000 0.000 0.018
> rs1807401 0.046 0.046 0.000 0.000 0.000 0.018
> rs1807402 0.046 0.046 0.000 0.000 0.000 0.018
> rs35350506 0.046 0.046 0.000 0.000 0.000 0.018
> rs1708626 rs1736206 rs9896078 rs16961474 rs1708627 rs1736205
> rs56192520 0.015 0.015 0.001 0.001 0.017 0.021
> rs3764410 0.013 0.013 0.001 0.001 0.014 0.019
> rs145984817 0.018 0.018 0.000 0.001 0.020 0.024
> rs1807401 0.018 0.018 0.000 0.001 0.020 0.024
> rs1807402 0.018 0.018 0.000 0.001 0.020 0.024
> rs35350506 0.018 0.018 0.000 0.001 0.020 0.024
> rs1708628 rs7220577 rs2294155 rs1736204 rs1736203 rs1736202
> rs56192520 0.011 0.011 0.000 0.021 0.014 0.014
> rs3764410 0.009 0.009 0.000 0.019 0.011 0.011
> rs145984817 0.013 0.013 0.001 0.024 0.016 0.016
> rs1807401 0.013 0.013 0.001 0.024 0.016 0.016
> rs1807402 0.013 0.013 0.001 0.024 0.016 0.016
> rs35350506 0.013 0.013 0.001 0.024 0.016 0.016
> rs12937908 rs1736200 rs1708623 rs1708624 rs9894884 rs9901894
> rs56192520 0.009 0.009 0.008 0.007 0.009 0.009
> rs3764410 0.007 0.007 0.006 0.005 0.007 0.007
> rs145984817 0.011 0.011 0.010 0.008 0.011 0.011
> rs1807401 0.011 0.011 0.010 0.008 0.011 0.011
> rs1807402 0.011 0.011 0.010 0.008 0.011 0.011
> rs35350506 0.011 0.011 0.010 0.008 0.011 0.011
> rs9903294 rs2472689 rs1630656 rs111478970 rs3182911 rs7219012
> rs56192520 0.008 0.011 0.007 0.007 0.008 0.000
> rs3764410 0.006 0.009 0.005 0.005 0.006 0.000
> rs145984817 0.010 0.013 0.008 0.008 0.010 0.001
> rs1807401 0.010 0.013 0.008 0.008 0.010 0.001
> rs1807402 0.010 0.013 0.008 0.008 0.010 0.001
> rs35350506 0.010 0.013 0.008 0.008 0.010 0.001
> rs9890657 rs12453455 rs12947291 rs150267386 rs16961493
rs11652745
> rs56192520 0.009 0.007 0.008 0.013 0.000
0.009
> rs3764410 0.007 0.005 0.006 0.012 0.000
0.007
> rs145984817 0.011 0.008 0.010 0.014 0.001
0.011
> rs1807401 0.011 0.008 0.010 0.014 0.001
0.011
> rs1807402 0.011 0.008 0.010 0.014 0.001
0.011
> rs35350506 0.011 0.008 0.010 0.014 0.001
0.011
> rs9907107 rs8070574 rs4985759 rs3866959 rs7219248 rs6502568
> rs56192520 0.009 0.009 0.009 0.011 0.009 0.011
> rs3764410 0.007 0.007 0.007 0.009 0.007 0.009
> rs145984817 0.011 0.011 0.011 0.013 0.011 0.013
> rs1807401 0.011 0.011 0.011 0.013 0.011 0.013
> rs1807402 0.011 0.011 0.011 0.013 0.011 0.013
> rs35350506 0.011 0.011 0.011 0.013 0.011 0.013
> rs7220275 rs12450037 rs7225876 rs9892352 rs4985760 rs6502569
> rs56192520 0.009 0.008 0.007 0.011 0.011 0.011
> rs3764410 0.007 0.006 0.005 0.009 0.009 0.009
> rs145984817 0.011 0.010 0.008 0.013 0.013 0.013
> rs1807401 0.011 0.010 0.008 0.013 0.013 0.013
> rs1807402 0.011 0.010 0.008 0.013 0.013 0.013
> rs35350506 0.011 0.010 0.008 0.013 0.013 0.013
> rs1029830 rs2012954 rs1029832 rs2270180 rs8072402 rs7221553
> rs56192520 0.009 0.011 0.008 0.000 0.009 0.011
> rs3764410 0.007 0.009 0.006 0.000 0.007 0.009
> rs145984817 0.011 0.013 0.010 0.001 0.011 0.013
> rs1807401 0.011 0.013 0.010 0.001 0.011 0.013
> rs1807402 0.011 0.013 0.010 0.001 0.011 0.013
> rs35350506 0.011 0.013 0.010 0.001 0.011 0.013
> rs145597919 rs150772017 rs2041393 rs6502578 rs11078382
rs9912109
> rs56192520 0.013 0.013 0.005 0.005 0
0.005
> rs3764410 0.012 0.012 0.004 0.004 0
0.004
> rs145984817 0.014 0.014 0.006 0.006 0
0.006
> rs1807401 0.014 0.014 0.006 0.006 0
0.006
> rs1807402 0.014 0.014 0.006 0.006 0
0.006
> rs35350506 0.014 0.014 0.006 0.006 0
0.006
> rs12601631 rs11869054 rs11869079 rs9912599 rs7220057 rs9896970
> rs56192520 0 0 0 0 0 0
> rs3764410 0 0 0 0 0 0
> rs145984817 0 0 0 0 0 0
> rs1807401 0 0 0 0 0 0
> rs1807402 0 0 0 0 0 0
> rs35350506 0 0 0 0 0 0
> rs34121330 rs34668117 rs67773570 rs242252 rs955893 rs28583584
> rs56192520 0.000 0.000 0 0.002 0.001 0.013
> rs3764410 0.001 0.001 0 0.003 0.001 0.005
> rs145984817 0.000 0.000 0 0.002 0.001 0.004
> rs1807401 0.000 0.000 0 0.002 0.001 0.004
> rs1807402 0.000 0.000 0 0.002 0.001 0.004
> rs35350506 0.000 0.000 0 0.002 0.001 0.004
> rs9944423 rs7217764 rs11651957 rs73978990 rs8071007 rs56044345
> rs56192520 0.013 0.011 0.011 0.011 0.011 0.011
> rs3764410 0.005 0.004 0.004 0.004 0.004 0.004
> rs145984817 0.004 0.003 0.003 0.003 0.003 0.003
> rs1807401 0.004 0.003 0.003 0.003 0.003 0.003
> rs1807402 0.004 0.003 0.003 0.003 0.003 0.003
> rs35350506 0.004 0.003 0.003 0.003 0.003 0.003
> rs17804843
> rs56192520 0
> rs3764410 0
> rs145984817 0
> rs1807401 0
> rs1807402 0
> rs35350506 0
>
>
> On Thu, Nov 14, 2019 at 2:59 PM Abby Spurdle <spurdle.a at gmail.com>
wrote:
> >
> > That's assuming your data was returned by head().
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.